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- PDB-6ksa: Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant fr... -

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Basic information

Entry
Database: PDB / ID: 6ksa
TitleCrystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C18CoA
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


: / long-chain acyl-CoA dehydrogenase / medium-chain acyl-CoA dehydrogenase / long-chain fatty acyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / medium-chain fatty acyl-CoA dehydrogenase activity / short-chain fatty acyl-CoA dehydrogenase activity / fatty acid metabolic process / flavin adenine dinucleotide binding / plasma membrane
Similarity search - Function
Acyl-CoA dehydrogenase, N-terminal, bacteria / : / Acetyl-CoA dehydrogenase-like C-terminal domain / Acetyl-CoA dehydrogenase C-terminal like / : / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / STEAROYL-COENZYME A / Acyl-CoA dehydrogenase / Broad-specificity linear acyl-CoA dehydrogenase FadE5
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.768 Å
AuthorsLiu, X. / Chen, X.B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria.
Authors: Chen, X. / Chen, J. / Yan, B. / Zhang, W. / Guddat, L.W. / Liu, X. / Rao, Z.
History
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,66511
Polymers133,6892
Non-polymers3,9769
Water20,7171150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12530 Å2
ΔGint-137 kcal/mol
Surface area38650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.934, 206.586, 74.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-1250-

HOH

21B-1272-

HOH

31B-1380-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acyl-CoA dehydrogenase


Mass: 66844.531 Da / Num. of mol.: 2 / Mutation: E447A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: fadE5, ERS451418_00380 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0D6G5A8, UniProt: Q3L887*PLUS, short-chain acyl-CoA dehydrogenase

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Non-polymers , 5 types, 1159 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-ST9 / STEAROYL-COENZYME A


Mass: 1033.996 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H70N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 0.1 M Hepes sodium (pH 7.0), 2% v/v PEG 400, 2 M (NH4)2SO4, 1 mM FAD and 1.2 mM C18CoA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.768→50 Å / Num. obs: 147197 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.056 / Rrim(I) all: 0.136 / Χ2: 0.952 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.84.70.86972210.6110.4360.9770.9799.6
1.8-1.835.50.77472890.7120.3550.8550.95499.8
1.83-1.875.70.68872420.7610.3110.7580.96299.9
1.87-1.915.70.60273200.8160.2710.6620.96599.9
1.91-1.955.70.52572940.8530.2380.5780.958100
1.95-1.995.70.45772910.8770.2080.5040.976100
1.99-2.045.40.3773150.9080.1740.4110.98199.9
2.04-2.15.50.32172750.9310.1490.3550.999100
2.1-2.165.90.2773040.9470.120.2961.003100
2.16-2.235.90.22473610.9630.10.2461.005100
2.23-2.315.80.19773070.9720.0880.2161.025100
2.31-2.45.60.17173490.9750.0780.1881.004100
2.4-2.515.40.14773200.980.0690.1630.99699.8
2.51-2.645.70.12673590.9860.0570.1390.98899.9
2.64-2.815.90.11173360.9880.0490.1220.98799.9
2.81-3.035.80.0973830.9910.040.0990.939100
3.03-3.335.40.06874400.9940.0320.0750.93399.9
3.33-3.815.90.05274560.9960.0230.0570.927100
3.81-4.85.50.03975150.9970.0180.0430.82399.8
4.8-505.40.03478200.9980.0150.0370.64699.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.768→45.683 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.03
RfactorNum. reflection% reflection
Rfree0.1714 7292 5.02 %
Rwork0.1488 --
obs0.1499 145200 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 287.85 Å2 / Biso mean: 26.0235 Å2 / Biso min: 11.07 Å2
Refinement stepCycle: final / Resolution: 1.768→45.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9329 0 450 1150 10929
Biso mean--32.23 34.22 -
Num. residues----1218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149773
X-RAY DIFFRACTIONf_angle_d1.20413250
X-RAY DIFFRACTIONf_dihedral_angle_d9.4235700
X-RAY DIFFRACTIONf_chiral_restr0.0681453
X-RAY DIFFRACTIONf_plane_restr0.011694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7682-1.78830.26862180.2352405988
1.7883-1.80930.27552010.2235427692
1.8093-1.83140.25792250.2079437995
1.8314-1.85460.21522400.2008441696
1.8546-1.8790.22892470.1932447397
1.879-1.90470.22392490.1877448097
1.9047-1.93190.23032380.1756454798
1.9319-1.96070.18542740.1688451398
1.9607-1.99140.18762500.1717456299
1.9914-2.0240.19692290.1691454699
2.024-2.05890.18842570.1626461499
2.0589-2.09640.19012400.15354609100
2.0964-2.13670.1762500.14584634100
2.1367-2.18030.18592340.14254654100
2.1803-2.22770.17242240.13944662100
2.2277-2.27950.16912450.13364605100
2.2795-2.33650.17982270.13374664100
2.3365-2.39970.17532530.1354641100
2.3997-2.47030.18322380.1394645100
2.4703-2.550.15032410.13014657100
2.55-2.64120.16262340.12864672100
2.6412-2.74690.16022550.13274636100
2.7469-2.87190.16682480.1364667100
2.8719-3.02330.15162750.14074624100
3.0233-3.21270.16222410.14514707100
3.2127-3.46060.1382480.13864705100
3.4606-3.80870.15092520.13914728100
3.8087-4.35950.13642600.1244741100
4.3595-5.4910.1482480.13324797100
5.491-45.6830.21862510.201499599

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